-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_7572223-7716412

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for CodingQuarry_transcript_46207-T1
Valid prediction for pasa_asmbl_40164.p1
Valid prediction for HiQ_model.g4459.t1
Valid prediction for snap_scaffold_3-snap.1541-T1
Valid prediction for snap_scaffold_3-snap.1569-T1
Valid prediction for GlimmerHMM_glimmerT_6856-T1
Valid prediction for snap_scaffold_3-snap.1562-T1
Valid prediction for snap_scaffold_3-snap.1555-T1
Valid prediction for snap_scaffold_3-snap.1543-T1
Valid prediction for GlimmerHMM_glimmerT_6840-T1
Valid prediction for GlimmerHMM_glimmerT_6851-T1
Valid prediction for CodingQuarry_transcript_46209-T1
Valid prediction for GlimmerHMM_glimmerT_6841-T1
Valid prediction for GlimmerHMM_glimmerT_6857-T1
Valid prediction for snap_scaffold_3-snap.1547-T1
Valid prediction for Augustus_model.g4458.t1
Valid prediction for snap_scaffold_3-snap.1549-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6852-T1
Valid prediction for snap_scaffold_3-snap.1566-T1
Valid prediction for Augustus_model.g4465.t1
Valid prediction for GlimmerHMM_glimmerT_6839-T1
Valid prediction for GlimmerHMM_glimmerT_6838-T1
Valid prediction for GlimmerHMM_glimmerT_6858-T1
Valid prediction for snap_scaffold_3-snap.1552-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6859-T1
Valid prediction for snap_scaffold_3-snap.1564-T1
Valid prediction for snap_scaffold_3-snap.1556-T1
Valid prediction for Augustus_model.g4462.t1
Valid prediction for CodingQuarry_transcript_46208-T1
Valid prediction for snap_scaffold_3-snap.1560-T1
Valid prediction for GlimmerHMM_glimmerT_6847-T1
Valid prediction for snap_scaffold_3-snap.1542-T1
Valid prediction for pasa_asmbl_40167.p1
Valid prediction for Augustus_model.g4471.t1
Valid prediction for Augustus_model.g4469.t1
Valid prediction for snap_scaffold_3-snap.1551-T1
Valid prediction for Augustus_model.g4463.t1
Valid prediction for snap_scaffold_3-snap.1572-T1
Valid prediction for GlimmerHMM_glimmerT_6855-T1
Valid prediction for Augustus_model.g4470.t1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for CodingQuarry_transcript_46212-T1
Valid prediction for Augustus_model.g4461.t1
Valid prediction for snap_scaffold_3-snap.1544-T1
Valid prediction for GlimmerHMM_glimmerT_6860-T1
Valid prediction for snap_scaffold_3-snap.1548-T1
Valid prediction for GlimmerHMM_glimmerT_6846-T1
Valid prediction for pasa_asmbl_38973.p1
Valid prediction for GlimmerHMM_glimmerT_6854-T1
Valid prediction for HiQ_model.g4468.t1
Valid prediction for GlimmerHMM_glimmerT_6848-T1
Valid prediction for snap_scaffold_3-snap.1563-T1
Valid prediction for snap_scaffold_3-snap.1568-T1
Valid prediction for snap_scaffold_3-snap.1565-T1
Valid prediction for GlimmerHMM_glimmerT_6845-T1
Valid prediction for snap_scaffold_3-snap.1554-T1
Valid prediction for snap_scaffold_3-snap.1539-T1
Valid prediction for snap_scaffold_3-snap.1571-T1
Valid prediction for snap_scaffold_3-snap.1561-T1
Valid prediction for Augustus_model.g4466.t1
Valid prediction for snap_scaffold_3-snap.1553-T1
Valid prediction for GlimmerHMM_glimmerT_6850-T1
Valid prediction for snap_scaffold_3-snap.1546-T1
Valid prediction for Augustus_model.g4467.t1
Valid prediction for GlimmerHMM_glimmerT_6853-T1
Valid prediction for pasa_asmbl_38976.p1
Valid prediction for snap_scaffold_3-snap.1540-T1
Valid prediction for snap_scaffold_3-snap.1558-T1
Couldn't classify 86936, 87439
Sorry, prediction pasa_asmbl_38971.p1 fails validation.
(CAG)	 CC	86936-87439	GG	ATG
Valid prediction for GlimmerHMM_glimmerT_6842-T1
Valid prediction for CodingQuarry_transcript_46211-T1
Valid prediction for snap_scaffold_3-snap.1570-T1
Valid prediction for snap_scaffold_3-snap.1567-T1
Valid prediction for GlimmerHMM_glimmerT_6844-T1
Valid prediction for snap_scaffold_3-snap.1545-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.1557-T1
Valid prediction for snap_scaffold_3-snap.1559-T1
Valid prediction for GlimmerHMM_glimmerT_6843-T1
Valid prediction for HiQ_model.g4472.t1
Valid prediction for snap_scaffold_3-snap.1550-T1
Valid prediction for Augustus_model.g4464.t1
Valid prediction for GlimmerHMM_glimmerT_6849-T1
Valid prediction for Augustus_model.g4460.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20408, rend_intergenic: 16583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32374, rend_intergenic: 30044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34420, rend_intergenic: 32441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44974, rend_intergenic: 34851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45920, rend_intergenic: 45295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50409, rend_intergenic: 46397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57463, rend_intergenic: 50623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75633, rend_intergenic: 73452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90530, rend_intergenic: 86607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96247, rend_intergenic: 91351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103767, rend_intergenic: 102405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106811, rend_intergenic: 104183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123892, rend_intergenic: 108907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133044, rend_intergenic: 127871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141223, rend_intergenic: 138657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 144190
-exon list size: 332


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 20408, rend_intergenic: 16583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32374, rend_intergenic: 30044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34420, rend_intergenic: 32441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44974, rend_intergenic: 34851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45920, rend_intergenic: 45295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50409, rend_intergenic: 46397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57463, rend_intergenic: 50623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75633, rend_intergenic: 73452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90530, rend_intergenic: 86607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96247, rend_intergenic: 91351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103767, rend_intergenic: 102405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106811, rend_intergenic: 104183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123892, rend_intergenic: 108907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133044, rend_intergenic: 127871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141223, rend_intergenic: 138657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support